Regulation of gene

expression
Premedical - Biology
Regulation of gene expression
in prokaryotic cell
• Operon units with genes for enzymes, proteins of one
metabolic pathway
• system of negative feedback
• positive and negative regulation

in eukaryotic cell
• at any stage of gene expression and proteosynthesis.
• Non-coding RNAs play roles in the regulation.
Transcription and translation
In bacterial cells:
Transcription and translation is coupled.
mRNA is immediately translated without
processing.

In Eukaryotic cell
The nucleus provides a separate
compartment for a transcription.
The pre-mRNA is processed in various ways
before leaving nucleus as mRNA
Translation of eukaryotes occurs in
cytoplasm.
Regulation of gene expression
in Prokaryotes = Operon model
Operon = functional, transcription and regulatory
unit
• contains cluster of genes (for enzymes of the particular
metabolic pathway), which are transcribed into one
mRNA (= polycistronic transcript)
• They are regulated by common promotor
• Prokaryotic genes have no introns (non-coding parts)
Escherichia coli

Lac operon, Trp operon – model systems =

metabolic pathways of
• utilization of lactose gen lacZ, lacY, lacA,

catabolic pathway with negative and positive

regulation

• enzymes for TRP synthesis, anabolic pathway

with negative regulation
 Operon
Gene expression – activation or inhibition of transcription is
regulated in respond to conditions in environment: presence
of substrates or products of metabolic pathways = effector
molecules

Effector molecules react with regulatory proteins (regulatory

gene products) and their complexes activate or repress the
transcription.
Regulatory proteins: Activators – positive control
Repressor – negative control
Effector molecules: inducers (induction)
corepressors (repression)
Positive and negative regulation of gene
expression

Positive = product of regulatory gene, activator, activates

transcription of structural genes protein

Negative = product of regulatory gene, repressor,

suppresses expression of structural genes
Effector molecules: the bond between them and
regulatory proteins changes their ability to bind to the
operator

inducer = molecule of substrate, which binds to active

repressor to block it up = transcription is possible

corepressor = the bond between corepressor and

product of metabolic reaction inhibits the transcription
(inactive repressor alone is not able to suppres
transcription)
Tryptophan operon

Repressor
Tryptofan -
corepressor

RNAP
Lac operon
- negative
regulation

Repressor

Lactose - inducer

RNAP
 Lac operon - negative regulation
means the presence of repressor, which is in active state and binds
operator and causes that RNAP is not able to initialize transcription.

Effector molecule is lactose (allolactose), which works as an inducer.

It binds a repressor and turns it into inactive state.
Lactose (allolactose) cause induction (activation) of transcription.
RNA polymerase starts the transcription. In 2-3 minutes the amount of
enzymes is increased 1000x
Lac operon - positive regulation

CAP – Catabolite activator protein

(cAMP receptor protein-CRP)

cAMP - inducer

RNAP
 Lac operon - positive regulation

• In the presence of glucose, E. coli preferentially uses the

glucose for a production of energy.
• If the level of glucose is low, the level of cAMP is high.
• CAP „Catabolite activator protein“ in the presence of
cAMP attaches the promotor and allows the RNAP to start
transcription.
• CAP is allosteric regulatory protein;
it is activated by cAMP = inducer
Gene expression of eukaryotic cells
• each cell maintains specific program/
differential gene expression
• one mRNA carries information for one gene
(monocistronic mRNA)
• post-transcriptional modifications of RNA,
RNA processing and splicing
• regulation system is performed at several
levels = transcription, translation, protein
activation + secretion
Levels of regulation of gene expression in euk. cell
 Disturbance of regulatory system

• chromatin changes
• transcription
• processing RNA
• transport to cytoplasm
• degradation of mRNA
• translation
• cleavage, chemical modification
• protein degradation
1. Chromatin changes

Role of DNA methylation and histone modification:

• In active chromatin – DNA (promoter) is demethylated,

histones are acetylated

• In inactive chromatin - DNA is methylated (promoter)

and histone de-acetylated
• Histone acetylation removes positive charge of histones –
thus reducing the force of attraction with electronegative
DNA = open chromatin (active)

• Deacetylation of histones restores positive charge of

histones leading to close attraction between histones and
DNA and to condensed chromatin structure = inactive =
i.e. inaccessible to transcription factors

• First step in gene inactivation = methylation of promoter

attracts complex containing histone deacetylase - it
starts gene inactivation
 Epigenetic regulation of gene expression
 DNA methylation, histone modification
Heterochromatin (inactive chromatin) is highly methylated
DNA methylation is essential for long-term inactivation of genes
during cell differentiation

Steps of gene inactivation: methylation of promoter,

deacetylation of histones, rearrangement of chromatin
to inactive state – inaccessible to transcription factors

 Role of non-coding RNAs in posttranscriptional regulation

of gene expression (destroying mRNA before translation)
 Gene imprinting = certain genes are expressed in a
parent-of-origin-specific manner - in mammals

= only one allele of specific parental origin is active,

second one is inactive = imprinted
Imprinting is connected with promoter methylation, histone
modification and chromatin rearrangement to inactive state

Imprinted genes in early human embryogenesis:

paternally expressed genes are responsible for placental
proliferation and invasiveness
maternally expressed genes are responsible for
development of embryo
 one hundred
and twenty
(120) human
imprinted genes
(confirmed by
experimental
evidences)
 2. Transcription
Transcription factors = positive and negative regulation
of transcription of eukaryotic genes (to facilitate
or inhibit)
Transcription factors:
general transcription factors for all protein-coding genes
specific transcription factors – transcription of particular
genes at specific time and place (in certain cell types
or in response to signals)

promoter, enhancers and silencers = regulatory DNA

elements (outside or inside gene)
Eukaryotic gene and transcript
Action of enhancers and transcription activators
Cell-type specific transcription:
Genes encoding enzymes of one metabolic pathway are
scattered over the different chromosomes –
• coordinated control in response of chemical signals
from outside environment.
• The cell accepts signals by receptors.
Signal transduction pathways activate transcription
activators or repressors.
3. RNA processing

Post-transcriptional modifications:
Splicing and alternative splicing
= the same primary RNA transcript, but different mRNA
molecule from it (exons are either retained in the
mRNA or targeted for removal in different
combinations to create a diverse array of mRNAs)
By alternative splicing we can make more than one
polypeptide from one gene
Alternative RNA splicing
For example, the 5' AMP-activated protein kinase (AMPK),
an enzyme, which performs different roles in human cells,
has 3 subunits:

α, catalytic domain, has two isoforms: α1 and α2 which are

encoded from PRKAA1 and PRKAA2
β, regulatory domain, has two isoforms: β1 and β2 which are
encoded from PRKAB1 and PRKAB2
γ, regulatory domain, has three isoforms: γ1, γ2, and γ3
which are encoded from PRKAG1, PRKAG2, and PRKAG3

In human skeletal muscle, the preferred form is α2β2γ1.

But in the human liver, the most abundant form is α1β2γ1.
Posttranscriptional regulation of gene expression:
some microRNAs = small non-coding regulatory RNAs that
can cut or can block mRNA to be translated
miRNAs interact with specific mRNAs to influence the
translation or stability of the target mRNA = epigenetic
mechanism

4, 5. transport of mRNA / degradation

A lifespan of mRNA is important for protein synthesis
6. Translation
At the initiation stage – regulatory proteins bind the 5’ end
of mRNA with the cap.
Activation or inactivation of protein factors to initiate
translation
 7. Cleavage, chemical modifications
Post-translational modifications of proteins
= chemical changes of proteins after translation,
proteolytic cleavage of regulatory subunits,
or degradation of entire proteins

Chemical modifications:
phosphorylation, glycosylation, ubiquitination, nitrosylation,
methylation, acetylation, lipidation and proteolysis
→ regulation of activity, localization, targeting and interaction
with other cellular molecules such as proteins, nucleic acids,
lipids…
Cleavage of polypeptide

• Polypeptide chain may

be cleaved into two or
three pieces
• Preproinsulin
• Proinsulin - disulfide
bridges
• Insulin
• Secretory protein
Post-translational modifications

Acid/base - act/inact
Hydrolysis – localization, act/inact
Acetylation - act/inact
Phosphorylation - act/inact
Prenylation - localization
Glycosylation - targeting
 Post-translational modifications
Phosphorylation plays critical roles in the regulation of many
cellular processes, including cell cycle, growth,
apoptosis and signal transduction pathways
Kinase – phosphorylation = binding of phosphate group
to a protein.
Phosphatase removes a phosphate group from a
protein. (dephosphorylation)
Both modulate activities of proteins in a cell, often in response
to external stimuli.
 Various steps in the synthesis and
assembly of collagen fibrils

Molecular Biology of the Cell, Third Edition , by Alberts, Bray, Lewis, Raff, Roberts, Watson (eds). Reproduced by permission of
Routledge, Inc., part of The Taylor & Francis Group.
8. protein degradation
A lifespan of protein is strictly regulated
Protein for destruction links to a small protein ubiquitin. Protein
complexes proteasomes are places of degradation.
 Thank you for your attention

Campbell, Neil A., Reece, Jane B., Cain Michael L., Jackson,
Robert B., Minorsky, Peter V., Biology, Benjamin-Cummings
Publishing Company, 1996 –2010.